Scripts for analysis of Auger Electron Spectroscopy data (geared towards PHI Auger Nanoprobe data but applicable to any Auger spectral data)

This set of python scripts/function can be used for:

• Batch import conversion of .sem, .spe and .map Auger files generated by PHI 700 Auger Nanoprobe (and related PHI instruments).
• Automatic combining via averaging of multiple Auger files on same samples (multiple spe files from same region generated using the Autotool loops with the PHI smartsoft control software)
• Batch smooth-differentiation of chosen element peaks and subsequent quantitative analysis (similar functionality to PHI Multipak software but can be run in batch mode on all files in given directory);
• Background fitting, peak subtraction and integration of direct counts signal (alternate quantization method that doesn’t rely on smoothing-differentiation)
• Plotting of individual spe files or creation of PDF batch reports containing all spectra in directory
• Source data along with background fits, peak fits, etc. are stored separately as CSV file and are thus accessible to any other plotting software
• Auger spectral imaging (using PHI multiplex mode and Autotool)

See AugerQuant_software_manual.pdf for how to use these scripts (includes around 10 pages of details and typical data processing pipeline). You can also view all of the functions in the various loaded modules (named AES**_functions.py).
Soon I'll create a video to demonstrate how infinitely faster and more organized these scripts are (compared with using PHI Multipak/Excel/some plotting software), since you might be slightly discouraged after glancing at *main.py files.

Note that your original spectral files are never modified (although sometimes moved to /sub directory)